Previously, we developed a highly sensitive assay for viremia, capable of detecting a single copy of HIV-1 RNA in plasma. This sensitivity, capable of quantitating virions in plasma down to 0.3 copies RNA/ml or less, represents a 150-fold improvement over previous ultra-sensitive assays. In collaboration with colleagues at Abbott Laboratories, we have found that viremia in patients is independent of regimen, but strongly associated with pretherapy virus levels, implying that, even after 7 years of treatment, cells infected prior to therapy survive to make more virus. These studies are being extended in clinical trials performed at NIH and elsewhere to ask what the decay rates of such cells are, and what happens to the levels if the treatment regimen is either simplified or intensified during therapy. We have adapted the single genome sequencing technique to study genetic variation in patients with suppressed viral RNA levels (in collaboration with Drs. Michael Polis and Deborah Persaud, NIH Bench to Bedside Award, 2006). The same assay is being used (in collaboration with Dr. Bruce Walker) to probe the levels of viremia in the rare HIV-1-infected patients who are able to control their viremia at very low levels in the absence of therapy, as well as in a well-described NIH cohort of patients with HLA-restricted HIV-1 replication (with Drs. Stephen Migueles, Mark Conners, and H. Clifford Lane) and also (in collaboration with Dr. David Margolis) to see whether a drug that activates HIV expression (i.e., valproic acid) can affect the level of persistent virus. [Corresponds to Project 1 in the April 2007 site visit report of the Host-Virus Interaction Unit, HIV Drug Resistance Program]